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Gameplay is most similar to Shining in the Darkness; the player explores towns and dungeons in the first-person view, with battles almost exclusively taking place in dungeons. Battles take place in a turn-based format, maintaining the first-person view but also allowing the player to view allies as they take their actions. One unique mechanic is the "pixie" system, where the player can befriend pixies that will attack enemies as the party encounters them.

Three mercenaries - Arthur, Melody, and Forte - are hired by the King of Enrich to hunt down and capture a renegade ninja by the name of Rodi. The group pursues Rodi to the nearby mines where, after a brief skirmish, an unknown craft crashes through the roof. All four characters are gravely injured, but soon healed by being possessed by strange spirits. While those inhabiting Arthur, Melody and Rodi seem benevolent, Forte is occupied by an evil spirit. From here the story follows the three unwitting heroes as they fight to stop the revival of the legendary 1,000 year kingdom, which would return the world to an age of darkness.[2]

Shining the Holy Ark takes place 20 years before Shining Force III. While in the town of Enrich, Arthur and the others meet a young boy named Julian. He tells them that his father went to investigate a haunted mansion in the woods, but never returned. Since that time he has been in the care of a family friend. It would later be discovered that Julian's father was killed by Galm, one of the mythical Vandals that ruled over the world during the time of the 1,000 year kingdom. His father's death compels Julian to seek revenge against Galm, which sets into motion his involvement in the events of Shining Force III.[3]

Rilix - a Vandal who secured a position as the king's advisor and court wizard; seeks the revival of the 1,000 year kingdom. One of the games major antagonists.

Sabato - A sage who served as the king's advisor and chancellor before being ousted by Rilix. He is responsible for summoning Galm back to the mortal realm, and in return Galm told him what would soon happen at Godspeak. Despite being stripped of his political power, Sabato seeks to manipulate that course of events so that good will triumph over evil.

Lord of the Far East Village - An elder who serves as leader of Far East Village. He is also the father of Rodi and Akane, and adoptive father of Panzer. He provides help and advice for the party in their struggle against Rilix.

Galm - the most powerful Vandal, yet for unknown reasons does not wish to see the 1,000 year kingdom revived, which puts him at odds with his brethren.

The story of Shining the Holy Ark was designed with a more mature audience in mind than earlier games in the Shining series were targeted towards. In a 2009 interview, producer Hiroyuki Takahashi commented: "Until [Shining] Wisdom, the idea had been simply to develop a story that would attract a broad range of users. From Holy Ark on, the story and game were redesigned to focus on the Saturn players of the time. Japanese Saturn owners were generally in their late-teens or early-twenties. The age group had shifted away from children, so... the concept was 'fantasy that can be enjoyed by adults'. This new approach led to a darker, deeper world than we had been creating for the 'all ages' category prior to Holy Ark. We started to work on the plot of a story that would be appropriate in such a world."[4] The game's soundtrack was composed by Motoi Sakuraba, who later wrote the music for Shining Force III.